The 22-year-old netted again on the stroke of half-time with a powerful left-footed finish after Hyoran Kaue's assist.
It is also the second F1 victory for the Faenza-based squad, following Sebastian Vettel's equally unlikely win at the 2008 Italian Grand Prix.
It is the second time Jepchirchir has broken a world record over the distance. She registered her personal best of 1:05:06 in a mixed race three years ago in Ras Al Khaimah to set the world record, which only stood for eight months.
Djokovic immediately rushed over to check if she was okay and placed his hand on her back as the judge struggled for air. After a few minutes she was able to get up and walked off the court.
After a discussion of around 10 minutes between tournament referees and officials, Djokovic was disqualified from the match.
In Thursday's only other match, Sport Recife won 2-1 at Gremio thanks to goals either side of half-time from Patric Cabral and Iago Maidana. Pepe pegged a late goal back for the hosts. Enditem
The home side was seen as lacklustre in the encounter with Greece, but managed to pick up the pace against the much lower ranked Moldova after coach Matjaz Kek made a few changes to the starting line-up, according to the Slovenian Press Agency STA.
Emre Can (Front, L) of Germany vies with Alcantara Thiago of Spain during a UEFA Nations League match between Germany and Spain in Stuttgart, Germany, Sept. 3, 2020. (Xinhua)
"I just don't know what to say, it was really close to a perfect moment," Vetter told World Athletics.
In other matches on Sunday, Atletico Mineiro won 1-0 at Coritiba, Sport Recife beat Goias 2-1 at home, Gremio drew 1-1 at Atletico Goianiense, Vasco da Gama secured a 1-0 win at home to Athletico Paranaense and Palmeiras won 2-1 at Bragantino. Enditem
Chang'an Athletic is in Group B with Meizhou Kejia, Guizhou Hengfeng, Zhejiang Greentown, Liaoning Shenyang and Jiangxi Liansheng. All the Group B matches will be played in Meizhou, Guangdong province.